Changelog#

All notable changes to pyXenium are documented here.

Unreleased#

0.4.6 - 2026-05-20#

  • Add pyXenium.perturb as the lightweight SpatialPerturb Bridge for optional Perturb-seq reference projection handoffs without adding a core runtime dependency.

  • Document AI-Driven Spatial Pathologist via the external spatho package as an optional workflow bridge, without adding new pyXenium runtime code or dependencies.

  • Packaging cleanup: stop shipping _vendor/Gmi/.github/** workflow files inside the wheel; narrow _vendor/Gmi/* package-data to the R sources actually consumed at runtime.

  • Pin aiohttp>=3.9 (previously unpinned) to match the rest of the runtime-dependency hygiene.

  • Tighten supported Python range to >=3.11 so classifiers, runtime, and CI matrix agree with the floor set by zarr>=3.1 (zarr 3.x has never shipped a wheel for Python 3.10).

  • Expand CI Python matrix to 3.11–3.13 and remove the duplicate test.yml workflow.

  • Fix bare except: in multimodal.analysis.differential.get_rna_expr_df so non-AttributeError failures surface.

  • Plug fsspec handle leaks in io.xenium_artifacts.open_text (release on TextIOWrapper/GzipFile construction error) and in read_cell_feature_matrix_h5 (close the fsspec fileobj when h5py.File(fileobj, ...) fails before falling back to a local re-open).

  • Seed np.random.random in the SCILD CCI adapter; benchmark runs are now reproducible via a seed kwarg.

  • Add logger.warning(...) / logger.debug(...) to 15 silent except Exception: sites across multimodal/histoseg_lazyslide.py, multimodal/immune_resistance.py, and _topology_core.safe_to_parquet.

  • README: replace the self-contradicting pyXenium.spatho row in the features table with the actual entry point (build_spatho_manifest + external spatho package).

0.4.5 - 2026-05-08#

  • Switch the repository and package metadata from the prior non-commercial license to AGPL-3.0-only.

  • Add SPATHO AB as the declared maintainer in public package metadata and user-facing project docs.

  • Refresh scverse submission drafts and manuscript availability text so license and maintainer metadata stay consistent with the release.

0.4.4 - 2026-05-05#

  • Finalize the XeniumSlide rename across the public I/O surface, examples, tests, and docs while removing the legacy XeniumSData alias.

  • Refresh GitHub/PyPI-facing version text and installation snippets so the published package metadata matches the new slide-native API.

0.4.1 - 2026-04-26#

  • Complete the PDC Dardel Slurm validation for the contour-GMI Atera S1/S5 workflow across all 8 stages.

  • Add final contour-GMI biological readout: QC20, RNA-only, and no-coordinate stages support an S5/DCIS RNA program led by NIBAN1 and SORL1.

  • Document spatial-only and all-nonempty sensitivity behavior, including composition-driven contour context and QC sensitivity to low-cell contours.

  • Add PDC validation summaries and release documentation for the GitHub-only v0.4.1 release.

0.4.0 - 2026-04-26#

  • Add pyXenium.mechanostress as the seventh canonical public surface for morphology-derived mechanical stress analysis.

  • Support HNSCC-style prefixed Xenium artifacts, including *_cell_feature_matrix.h5, cells parquet, boundary parquet, and transcript parquet variants.

  • Add cohort-level mechanostress workflow APIs and CLI output summaries.

  • Add pyarrow as a runtime dependency so PyPI installs can read parquet-based Xenium exports directly.

0.3.0 - 2026-04-25#

  • Promote pyXenium.gmi to the sixth canonical public surface for contour-level GMI modeling.

  • Add contour-GMI API, tutorial, user-guide, and Atera reproducibility workflow documentation.

  • Expose core GMI types and workflow functions from the top-level pyXenium namespace.

  • Keep the vendored local Gmi R source as the only runtime installation source.

0.2.3 - 2026-04-22#

  • Add missing runtime dependencies required by the public import surface in clean environments, including seaborn, statsmodels, scanpy, and PyYAML.

  • Validate a clean-environment import pyXenium path after the rapid 0.2.2 hotfix.

0.2.2 - 2026-04-22#

  • Fix a cross-platform SyntaxError in pyXenium.io.xenium_artifacts.join_path(...) caused by a backslash-containing f-string expression.

  • Restore Linux CI importability immediately after the 0.2.1 metadata/docs sync release.

0.2.1 - 2026-04-22#

  • Add pyXenium.contour.expand_contours(...) with overlap-preserving and Voronoi-exclusive contour expansion modes.

  • Migrate the documentation site to Sphinx + pydata-sphinx-theme.

  • Rebuild the homepage and API landing pages around canonical public namespaces.

  • Add pyXenium branding assets for Read the Docs and GitHub surfaces.

  • Synchronize GitHub, Read the Docs, and PyPI cross-links, metadata, and build/version status displays.